6-90372562-C-T

Variant names:

• chr6-90372562-C-T
• rs6915865
• ENST00000741971.1:n.194+1598C>T

Variant summary

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

The ENST00000741971.1(ENSG00000296783):​n.194+1598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,004 control chromosomes in the GnomAD database, including 31,891 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 (31891 hom., cov: 32)
• Consequence: ENSG00000296783 ENST00000741971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 publications found

Genes affected

ENSG00000296783 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741971.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296783	ENST00000741971.1		n.194+1598C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97582 AN: 151886 Hom.: 31851 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.643 AC: 97675 AN: 152004 Hom.: 31891 Cov.: 32 AF XY: 0.649 AC XY: 48176 AN XY: 74288

African (AFR) AF: 0.694 AC: 28777 AN: 41440

American (AMR) AF: 0.652 AC: 9948 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1934 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5108 AN: 5172

South Asian (SAS) AF: 0.636 AC: 3062 AN: 4818

European-Finnish (FIN) AF: 0.667 AC: 7052 AN: 10566

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39772 AN: 67956

Other (OTH) AF: 0.648 AC: 1370 AN: 2114

Alfa AF: 0.612 Hom.: 44476

Bravo AF: 0.647

Asia WGS AF: 0.798 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6915865; hg19: chr6-91082281; COSMIC: COSV50464870;