ENST00000695747.1:c.493-1703G>A

Variant names:

• chr1-22641932-G-A
• rs4655085
• ENST00000695747.1:c.493-1703G>A

Variant summary

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

The ENST00000695747.1(ENSG00000289692):​c.493-1703G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,210 control chromosomes in the GnomAD database, including 2,636 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 0.16 (2636 hom., cov: 33)
• Consequence: ENSG00000289692 ENST00000695747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 6 publications found

Genes affected

ENSG00000289692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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
ENSG00000289692	ENST00000695747.1	c.493-1703G>A		intron_variant	Intron 3 of 4			ENSP00000512140.1
ENSG00000289692	ENST00000695748.1	c.493-2079G>A		intron_variant	Intron 3 of 3			ENSP00000512141.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23892 AN: 152092 Hom.: 2634 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.157 AC: 23933 AN: 152210 Hom.: 2636 Cov.: 33 AF XY: 0.158 AC XY: 11727 AN XY: 74436

African (AFR) AF: 0.313 AC: 12971 AN: 41500

American (AMR) AF: 0.0962 AC: 1473 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3470

East Asian (EAS) AF: 0.167 AC: 862 AN: 5166

South Asian (SAS) AF: 0.152 AC: 732 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5901 AN: 68010

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.125 Hom.: 212

Bravo AF: 0.162

Asia WGS AF: 0.157 AC: 546 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	3.4
DANN	Benign	0.28
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4655085; hg19: chr1-22968425;