rs7671167

Variant names:

• chr4-88962828-C-T
• rs7671167
• NM_014883.4:c.606-24587G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-88962828-C-T
• chr4-88962828-C-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014883.4(FAM13A):​c.606-24587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,860 control chromosomes in the GnomAD database, including 20,944 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.52 (20944 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -0.901
• Publications: 81 publications found

Genes affected

FAM13A (HGNC:19367): (family with sequence similarity 13 member A) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 4-88962828-C-T is Benign according to our data. Variant chr4-88962828-C-T is described in ClinVar as Benign. ClinVar VariationId is 1027618.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014883.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	NM_014883.4	MANE Select	c.606-24587G>A		intron	N/A	NP_055698.2	O94988-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM13A	ENST00000264344.10	TSL:5 MANE Select	c.606-24587G>A		intron	N/A	ENSP00000264344.5	O94988-4
	FAM13A	ENST00000511976.5	TSL:1	c.-22-24587G>A		intron	N/A	ENSP00000421914.1	E9PGM7
	FAM13A	ENST00000509094.5	TSL:1	c.606-24587G>A		intron	N/A	ENSP00000426517.1	D6RFM4

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79664 AN: 151744 Hom.: 20921 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.525 AC: 79725 AN: 151860 Hom.: 20944 Cov.: 32 AF XY: 0.521 AC XY: 38682 AN XY: 74210

African (AFR) AF: 0.597 AC: 24724 AN: 41396

American (AMR) AF: 0.504 AC: 7691 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.530 AC: 2736 AN: 5166

South Asian (SAS) AF: 0.447 AC: 2148 AN: 4806

European-Finnish (FIN) AF: 0.498 AC: 5250 AN: 10540

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34282 AN: 67904

Other (OTH) AF: 0.490 AC: 1031 AN: 2106

Alfa AF: 0.498 Hom.: 84592

Bravo AF: 0.527

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	-	Chronic obstructive pulmonary disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.57
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7671167; hg19: chr4-89883979;