NM_182623.3:c.23-3226A>C

Variant names:

• chr1-16066862-T-G
• rs9442235
• NM_182623.3:c.23-3226A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182623.3(FAM131C):​c.23-3226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,086 control chromosomes in the GnomAD database, including 19,041 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (19041 hom., cov: 33)
• Consequence: FAM131C NM_182623.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 19 publications found

Genes affected

FAM131C (HGNC:26717): (family with sequence similarity 131 member C)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM131C	NM_182623.3	c.23-3226A>C		intron_variant	Intron 1 of 6	ENST00000375662.5	NP_872429.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM131C	ENST00000375662.5	c.23-3226A>C		intron_variant	Intron 1 of 6	1	NM_182623.3	ENSP00000364814.4
FAM131C	ENST00000494078.1	n.213-4328A>C		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74363 AN: 151968 Hom.: 19013 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.489 AC: 74426 AN: 152086 Hom.: 19041 Cov.: 33 AF XY: 0.482 AC XY: 35847 AN XY: 74342

African (AFR) AF: 0.559 AC: 23199 AN: 41476

American (AMR) AF: 0.506 AC: 7736 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2001 AN: 3464

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5180

South Asian (SAS) AF: 0.460 AC: 2224 AN: 4830

European-Finnish (FIN) AF: 0.391 AC: 4132 AN: 10568

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33389 AN: 67964

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.491 Hom.: 80682

Bravo AF: 0.500

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-1.0
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: rs9442235; hg19: chr1-16393357;