rs2842063

Variant names:

• chr6-70528674-C-T
• rs2842063
• NM_001162529.3:c.3775+222C>T

Variant summary

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

The NM_001162529.3(FAM135A):​c.3775+222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 150,564 control chromosomes in the GnomAD database, including 16,129 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 0.37 (16129 hom., cov: 31)
• Consequence: FAM135A NM_001162529.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 3 publications found

Genes affected

FAM135A (HGNC:21084): (family with sequence similarity 135 member A) Predicted to be involved in cellular lipid metabolic process. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001162529.3. 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
	FAM135A	NM_001162529.3	MANE Select	c.3775+222C>T		intron	N/A	NP_001156001.1
	FAM135A	NM_001330996.3		c.3853+222C>T		intron	N/A	NP_001317925.1
	FAM135A	NM_001330999.3		c.3853+222C>T		intron	N/A	NP_001317928.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM135A	ENST00000418814.7	TSL:5 MANE Select	c.3775+222C>T		intron	N/A	ENSP00000410768.2
	FAM135A	ENST00000370479.7	TSL:1	c.3775+222C>T		intron	N/A	ENSP00000359510.4
	FAM135A	ENST00000361499.7	TSL:1	c.3187+222C>T		intron	N/A	ENSP00000354913.3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55070 AN: 150450 Hom.: 16075 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.0663

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.367 AC: 55188 AN: 150564 Hom.: 16129 Cov.: 31 AF XY: 0.363 AC XY: 26670 AN XY: 73376

African (AFR) AF: 0.813 AC: 33660 AN: 41384

American (AMR) AF: 0.270 AC: 4063 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 391 AN: 3438

East Asian (EAS) AF: 0.0965 AC: 490 AN: 5080

South Asian (SAS) AF: 0.168 AC: 782 AN: 4656

European-Finnish (FIN) AF: 0.251 AC: 2555 AN: 10178

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12438 AN: 67530

Other (OTH) AF: 0.323 AC: 668 AN: 2066

Alfa AF: 0.213 Hom.: 7320

Bravo AF: 0.383

Asia WGS AF: 0.226 AC: 787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.34
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: rs2842063; hg19: chr6-71238377;