rs169715

Variant names:

• chr6-11938564-G-A
• rs169715
• ENST00000848130.1:n.334-12971G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-11938564-G-A
• chr6-11938564-G-C
• chr6-11938564-G-T

Variant summary

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

The ENST00000848130.1(ENSG00000310201):​n.334-12971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,270 control chromosomes in the GnomAD database, including 67,390 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 0.94 (67390 hom., cov: 32)
• Consequence: ENSG00000310201 ENST00000848130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 6 publications found

Genes affected

ENSG00000310201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986570	XR_001743976.2	n.362+4173G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310201	ENST00000848130.1	n.334-12971G>A		intron_variant	Intron 1 of 2
ENSG00000310201	ENST00000848131.1	n.238-12971G>A		intron_variant	Intron 1 of 2
ENSG00000310201	ENST00000848132.1	n.362+4173G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143108 AN: 152152 Hom.: 67348 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.940 AC: 143205 AN: 152270 Hom.: 67390 Cov.: 32 AF XY: 0.939 AC XY: 69886 AN XY: 74444

African (AFR) AF: 0.962 AC: 39965 AN: 41528

American (AMR) AF: 0.880 AC: 13455 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3128 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4985 AN: 5184

South Asian (SAS) AF: 0.875 AC: 4220 AN: 4824

European-Finnish (FIN) AF: 0.968 AC: 10280 AN: 10620

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64075 AN: 68034

Other (OTH) AF: 0.931 AC: 1968 AN: 2114

Alfa AF: 0.934 Hom.: 114162

Bravo AF: 0.934

Asia WGS AF: 0.920 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0090
DANN	Benign	0.47
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs169715; hg19: chr6-11938797;