rs6972429

Variant names:

• chr7-41855244-C-T
• rs6972429
• ENST00000839902.1:n.453-16764C>T

Variant summary

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

The ENST00000839902.1(ENSG00000309263):​n.453-16764C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,126 control chromosomes in the GnomAD database, including 37,429 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 0.69 (37429 hom., cov: 32)
• Consequence: ENSG00000309263 ENST00000839902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 0 publications found

Genes affected

ENSG00000309263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 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
ENSG00000309263	ENST00000839902.1	n.453-16764C>T		intron_variant	Intron 4 of 5
ENSG00000309263	ENST00000839903.1	n.246-16764C>T		intron_variant	Intron 3 of 3
ENSG00000309263	ENST00000839904.1	n.237-16764C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105181 AN: 152008 Hom.: 37371 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.692 AC: 105295 AN: 152126 Hom.: 37429 Cov.: 32 AF XY: 0.689 AC XY: 51233 AN XY: 74370

African (AFR) AF: 0.826 AC: 34305 AN: 41516

American (AMR) AF: 0.588 AC: 8986 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2260 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1874 AN: 5160

South Asian (SAS) AF: 0.667 AC: 3210 AN: 4816

European-Finnish (FIN) AF: 0.707 AC: 7486 AN: 10584

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44926 AN: 67982

Other (OTH) AF: 0.688 AC: 1448 AN: 2106

Alfa AF: 0.710 Hom.: 5766

Bravo AF: 0.685

Asia WGS AF: 0.592 AC: 2055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6972429; hg19: chr7-41894842;