6-97761473-C-T

Position:

• chr6-97761473-C-T

Variant summary

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

The ENST00000656098.1(ENSG00000271860):​n.1096+53669C>T 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 0.637 in 151,912 control chromosomes in the GnomAD database, including 31,356 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 0.64 (31356 hom., cov: 31)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656098.1	n.1096+53669C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96620 AN: 151794 Hom.: 31301 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.637 AC: 96723 AN: 151912 Hom.: 31356 Cov.: 31 AF XY: 0.637 AC XY: 47257 AN XY: 74216

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.634

Alfa AF: 0.584 Hom.: 28851

Bravo AF: 0.660

Asia WGS AF: 0.633 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1338551; hg19: chr6-98209349;