6-97761473-C-T

Variant names:

• chr6-97761473-C-T
• rs1338551
• ENST00000574739.2:n.1081+53669C>T

Variant summary

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

The ENST00000574739.2(ENSG00000271860):​n.1081+53669C>T variant causes a intron 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: ENSG00000271860 ENST00000574739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000574739.2	n.1081+53669C>T		intron_variant	Intron 6 of 6	4
ENSG00000271860	ENST00000653817.1	n.551+7702C>T		intron_variant	Intron 6 of 11
ENSG00000271860	ENST00000656098.1	n.1096+53669C>T		intron_variant	Intron 6 of 10

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

African (AFR) AF: 0.722 AC: 29906 AN: 41416

American (AMR) AF: 0.702 AC: 10704 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2475 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4104 AN: 5158

South Asian (SAS) AF: 0.517 AC: 2488 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5728 AN: 10544

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39092 AN: 67942

Other (OTH) AF: 0.634 AC: 1337 AN: 2110

Alfa AF: 0.592 Hom.: 37073

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1338551; hg19: chr6-98209349;