rs6951646

Variant names:

• chr7-21139308-G-A
• rs6951646
• ENST00000821909.1:n.383-19942C>T

Variant summary

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

The ENST00000821909.1(ENSG00000306908):​n.383-19942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,168 control chromosomes in the GnomAD database, including 1,973 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 0.13 (1973 hom., cov: 32)
• Consequence: ENSG00000306908 ENST00000821909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 4 publications found

Genes affected

ENSG00000306908 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 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
ENSG00000306908	ENST00000821909.1	n.383-19942C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20135 AN: 152050 Hom.: 1965 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.133 AC: 20166 AN: 152168 Hom.: 1973 Cov.: 32 AF XY: 0.128 AC XY: 9509 AN XY: 74388

African (AFR) AF: 0.270 AC: 11189 AN: 41494

American (AMR) AF: 0.0872 AC: 1333 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0901 AC: 313 AN: 3472

East Asian (EAS) AF: 0.160 AC: 830 AN: 5174

South Asian (SAS) AF: 0.0416 AC: 201 AN: 4826

European-Finnish (FIN) AF: 0.0415 AC: 440 AN: 10600

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0817 AC: 5558 AN: 68000

Other (OTH) AF: 0.114 AC: 240 AN: 2114

Alfa AF: 0.0912 Hom.: 413

Bravo AF: 0.142

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.21
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs6951646; hg19: chr7-21178927; COSMIC: COSV70887030;