6-163341937-T-C

Variant names:

• chr6-163341937-T-C
• rs760885
• ENST00000648606.2:n.2304A>G

Variant summary

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

The ENST00000648606.2(ENSG00000285564):​n.2304A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,004 control chromosomes in the GnomAD database, including 39,643 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 0.71 (39643 hom., cov: 31)
• Consequence: ENSG00000285564 ENST00000648606.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 2 publications found

Genes affected

ENSG00000285564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DKFZp451B082	NR_033862.1	n.2567A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285564	ENST00000648606.2	n.2304A>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000285564	ENST00000653903.1	n.2104A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285564	ENST00000659196.1	n.2116A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108536 AN: 151888 Hom.: 39574 Cov.: 31

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.715 AC: 108656 AN: 152004 Hom.: 39643 Cov.: 31 AF XY: 0.713 AC XY: 52974 AN XY: 74280

African (AFR) AF: 0.865 AC: 35879 AN: 41490

American (AMR) AF: 0.658 AC: 10053 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3468

East Asian (EAS) AF: 0.556 AC: 2863 AN: 5146

South Asian (SAS) AF: 0.672 AC: 3240 AN: 4822

European-Finnish (FIN) AF: 0.690 AC: 7285 AN: 10554

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44815 AN: 67938

Other (OTH) AF: 0.701 AC: 1481 AN: 2112

Alfa AF: 0.689 Hom.: 10477

Bravo AF: 0.718

Asia WGS AF: 0.671 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.24
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs760885; hg19: chr6-163762969; COSMIC: COSV69432212;