6-163341937-T-C

Position:

• chr6-163341937-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033862.1(DKFZp451B082):​n.2567A>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: DKFZp451B082 NR_033862.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DKFZp451B082	NR_033862.1	n.2567A>G		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648606.1	n.2304A>G		non_coding_transcript_exon_variant	3/4

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

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.701

Alfa AF: 0.683 Hom.: 7628

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

Splicing

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

Publications

LitVar

Other links and lift over

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