rs649395

Variant names:

• chr6-16776095-C-T
• rs649395
• ENST00000701188.2:n.85-4902G>A

Variant summary

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

The ENST00000701188.2(ENSG00000289863):​n.85-4902G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,956 control chromosomes in the GnomAD database, including 2,887 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 0.18 (2887 hom., cov: 32)
• Consequence: ENSG00000289863 ENST00000701188.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 4 publications found

Genes affected

ENSG00000289863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289863	ENST00000701188.2	n.85-4902G>A		intron_variant	Intron 1 of 4
ENSG00000289863	ENST00000840667.1	n.474+753G>A		intron_variant	Intron 3 of 6
ENSG00000289863	ENST00000840668.1	n.85-4902G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26634 AN: 151838 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.175 AC: 26635 AN: 151956 Hom.: 2887 Cov.: 32 AF XY: 0.177 AC XY: 13125 AN XY: 74252

African (AFR) AF: 0.0552 AC: 2288 AN: 41464

American (AMR) AF: 0.149 AC: 2274 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3472

East Asian (EAS) AF: 0.0940 AC: 487 AN: 5180

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4808

European-Finnish (FIN) AF: 0.281 AC: 2952 AN: 10496

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15804 AN: 67948

Other (OTH) AF: 0.194 AC: 409 AN: 2112

Alfa AF: 0.193 Hom.: 1247

Bravo AF: 0.159

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	18
DANN	Benign	0.66
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs649395; hg19: chr6-16776326;