rs706393

Variant names:

• chr1-56185349-T-A
• rs706393
• ENST00000641302.1:n.323-1729A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-56185349-T-A
• chr1-56185349-T-C

Variant summary

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

The ENST00000641302.1(ENSG00000260971):​n.323-1729A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,266 control chromosomes in the GnomAD database, including 1,165 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 0.071 (1165 hom., cov: 32)
• Consequence: ENSG00000260971 ENST00000641302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 0 publications found

Genes affected

ENSG00000260971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000260971	ENST00000641302.1	n.323-1729A>T		intron_variant	Intron 2 of 4
ENSG00000260971	ENST00000641348.1	n.303-1729A>T		intron_variant	Intron 2 of 7
ENSG00000260971	ENST00000641349.1	n.294-1729A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10720 AN: 152146 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0707 AC: 10759 AN: 152266 Hom.: 1165 Cov.: 32 AF XY: 0.0678 AC XY: 5052 AN XY: 74462

African (AFR) AF: 0.229 AC: 9507 AN: 41512

American (AMR) AF: 0.0273 AC: 418 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4830

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10624

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00588 AC: 400 AN: 68026

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0115 Hom.: 20

Bravo AF: 0.0790

Asia WGS AF: 0.0360 AC: 123 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.72
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs706393; hg19: chr1-56651021;