chr6-11938564-G-A

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848130.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310201	ENST00000848130.1		n.334-12971G>A		intron	N/A
	ENSG00000310201	ENST00000848131.1		n.238-12971G>A		intron	N/A
	ENSG00000310201	ENST00000848132.1		n.362+4173G>A		intron	N/A

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 v4.9

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;