rs1343657

Positions:

• chr6-126942389-T-C

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.693+61796A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,914 control chromosomes in the GnomAD database, including 12,276 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 0.39 (12276 hom., cov: 31)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377989	XR_002956387.2	n.3716-22743A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651326.1	n.693+61796A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58535 AN: 151796 Hom.: 12273 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.385 AC: 58556 AN: 151914 Hom.: 12276 Cov.: 31 AF XY: 0.391 AC XY: 29015 AN XY: 74222

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.391

Alfa AF: 0.394 Hom.: 2097

Bravo AF: 0.376

Asia WGS AF: 0.467 AC: 1624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343657; hg19: chr6-127263534; COSMIC: COSV69425753;