rs4122017

Variant names:

• chr6-147984816-T-C
• rs4122017
• ENST00000773311.1:n.49-33962T>C

Variant summary

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

The ENST00000773311.1(ENSG00000287976):​n.49-33962T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,066 control chromosomes in the GnomAD database, including 16,377 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 0.44 (16377 hom., cov: 32)
• Consequence: ENSG00000287976 ENST00000773311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 2 publications found

Genes affected

ENSG00000287976 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773311.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287976	ENST00000773311.1		n.49-33962T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67080 AN: 151948 Hom.: 16371 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.441 AC: 67104 AN: 152066 Hom.: 16377 Cov.: 32 AF XY: 0.445 AC XY: 33113 AN XY: 74338

African (AFR) AF: 0.215 AC: 8905 AN: 41490

American (AMR) AF: 0.476 AC: 7283 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3032 AN: 5156

South Asian (SAS) AF: 0.598 AC: 2883 AN: 4818

European-Finnish (FIN) AF: 0.531 AC: 5615 AN: 10568

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36148 AN: 67964

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.490 Hom.: 24944

Bravo AF: 0.421

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.27
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4122017;

hg19: chr6-148305952;

COSMIC: COSV60290667;