1-194339198-T-G

Variant names:

• chr1-194339198-T-G
• rs6663592
• ENST00000727217.1:n.499+15107A>C

Variant summary

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

The ENST00000727217.1(ENSG00000294997):​n.499+15107A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,058 control chromosomes in the GnomAD database, including 67,491 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 0.94 (67491 hom., cov: 33)
• Consequence: ENSG00000294997 ENST00000727217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 0 publications found

Genes affected

ENSG00000294997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727217.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294997	ENST00000727217.1		n.499+15107A>C		intron	N/A
	ENSG00000294997	ENST00000727218.1		n.502+15107A>C		intron	N/A
	ENSG00000294997	ENST00000727219.1		n.500+15107A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.941 AC: 142915 AN: 151940 Hom.: 67473 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.940 AC: 142987 AN: 152058 Hom.: 67491 Cov.: 33 AF XY: 0.942 AC XY: 70062 AN XY: 74352

African (AFR) AF: 0.846 AC: 35115 AN: 41490

American (AMR) AF: 0.970 AC: 14803 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3408 AN: 3464

East Asian (EAS) AF: 0.996 AC: 5166 AN: 5188

South Asian (SAS) AF: 0.980 AC: 4729 AN: 4824

European-Finnish (FIN) AF: 0.983 AC: 10439 AN: 10624

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66126 AN: 67902

Other (OTH) AF: 0.949 AC: 1999 AN: 2106

Alfa AF: 0.948 Hom.: 8876

Bravo AF: 0.935

Asia WGS AF: 0.968 AC: 3343 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.57
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6663592; hg19: chr1-194308328;