chr1-157250762-G-A

Variant names:

• chr1-157250762-G-A
• rs4097766
• ENST00000727371.1:n.604+1644C>T

Variant summary

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

The ENST00000727371.1(ENSG00000295014):​n.604+1644C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 152,116 control chromosomes in the GnomAD database, including 193 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 0.035 (193 hom., cov: 32)
• Consequence: ENSG00000295014 ENST00000727371.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 0 publications found

Genes affected

ENSG00000295014 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727371.1. 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
	ENSG00000295014	ENST00000727371.1		n.604+1644C>T		intron	N/A
	ENSG00000295014	ENST00000727372.1		n.574+1644C>T		intron	N/A
	ENSG00000295014	ENST00000727373.1		n.510+1644C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5356 AN: 152000 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0353 AC: 5370 AN: 152116 Hom.: 193 Cov.: 32 AF XY: 0.0363 AC XY: 2703 AN XY: 74374

African (AFR) AF: 0.0403 AC: 1672 AN: 41504

American (AMR) AF: 0.0990 AC: 1511 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.0810 AC: 419 AN: 5176

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4812

European-Finnish (FIN) AF: 0.0108 AC: 114 AN: 10580

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1241 AN: 67988

Other (OTH) AF: 0.0299 AC: 63 AN: 2110

Alfa AF: 0.0121 Hom.: 1

Bravo AF: 0.0429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4097766;

hg19: chr1-157220552;