3-195017144-T-G

Variant names:

• chr3-195017144-T-G
• rs2676917
• ENST00000767547.1:n.167-1947T>G

Variant summary

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

The ENST00000767547.1(ENSG00000299931):​n.167-1947T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,830 control chromosomes in the GnomAD database, including 18,190 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 0.46 (18190 hom., cov: 30)
• Consequence: ENSG00000299931 ENST00000767547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 5 publications found

Genes affected

ENSG00000299931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767547.1. 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
	ENSG00000299931	ENST00000767547.1		n.167-1947T>G		intron	N/A
	ENSG00000299931	ENST00000767548.1		n.236-1947T>G		intron	N/A
	ENSG00000299931	ENST00000767549.1		n.142-1947T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69741 AN: 151712 Hom.: 18187 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.459 AC: 69751 AN: 151830 Hom.: 18190 Cov.: 30 AF XY: 0.459 AC XY: 34041 AN XY: 74138

African (AFR) AF: 0.205 AC: 8504 AN: 41406

American (AMR) AF: 0.535 AC: 8165 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1624 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1642 AN: 5166

South Asian (SAS) AF: 0.410 AC: 1968 AN: 4798

European-Finnish (FIN) AF: 0.613 AC: 6429 AN: 10494

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39857 AN: 67948

Other (OTH) AF: 0.480 AC: 1007 AN: 2100

Alfa AF: 0.537 Hom.: 89747

Bravo AF: 0.444

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.91

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: rs2676917;

hg19: chr3-194737873;