rs6935954

Positions:

• chr6-26255223-A-G
• chr6-26255223-A-T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+131052A>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 0.716 in 152,164 control chromosomes in the GnomAD database, including 40,604 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 0.72 (40604 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707189.1	n.999+131052A>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+97102A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108844 AN: 152046 Hom.: 40553 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.716 AC: 108958 AN: 152164 Hom.: 40604 Cov.: 32 AF XY: 0.723 AC XY: 53774 AN XY: 74374

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.736

Alfa AF: 0.621 Hom.: 41525

Bravo AF: 0.725

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935954; hg19: chr6-26255451;