rs6965643

Variant names:

• chr7-129767724-A-G
• rs6965643
• ENST00000660838.2:n.591+163T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-129767724-A-G
• chr7-129767724-A-T

Variant summary

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

The ENST00000660838.2(ENSG00000286380):​n.591+163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,012 control chromosomes in the GnomAD database, including 7,096 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 0.28 (7096 hom., cov: 32)
• Consequence: ENSG00000286380 ENST00000660838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 12 publications found

Genes affected

ENSG00000286380 (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 (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375501	XR_927963.4	n.590+163T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286380	ENST00000660838.2	n.591+163T>C		intron_variant	Intron 2 of 2
ENSG00000286380	ENST00000704489.2	n.1041+163T>C		intron_variant	Intron 1 of 2
ENSG00000286380	ENST00000704490.1	n.368+163T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42997 AN: 151894 Hom.: 7077 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.283 AC: 43052 AN: 152012 Hom.: 7096 Cov.: 32 AF XY: 0.292 AC XY: 21684 AN XY: 74300

African (AFR) AF: 0.331 AC: 13718 AN: 41428

American (AMR) AF: 0.349 AC: 5334 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3926 AN: 5146

South Asian (SAS) AF: 0.392 AC: 1889 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2866 AN: 10570

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13845 AN: 67988

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.234 Hom.: 14363

Bravo AF: 0.294

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6965643; hg19: chr7-129407564;