rs1905261

Variant names:

• chr4-155581126-C-A
• rs1905261
• ENST00000730967.1:n.270-11360C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-155581126-C-A
• chr4-155581126-C-G
• chr4-155581126-C-T

Variant summary

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

The ENST00000730967.1(ENSG00000251244):​n.270-11360C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,828 control chromosomes in the GnomAD database, including 19,731 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 0.51 (19731 hom., cov: 31)
• Consequence: ENSG00000251244 ENST00000730967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 4 publications found

Genes affected

ENSG00000251244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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
ENSG00000251244	ENST00000730967.1	n.270-11360C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76665 AN: 151710 Hom.: 19727 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.505 AC: 76715 AN: 151828 Hom.: 19731 Cov.: 31 AF XY: 0.515 AC XY: 38208 AN XY: 74202

African (AFR) AF: 0.423 AC: 17510 AN: 41372

American (AMR) AF: 0.511 AC: 7782 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3468

East Asian (EAS) AF: 0.729 AC: 3757 AN: 5156

South Asian (SAS) AF: 0.609 AC: 2931 AN: 4816

European-Finnish (FIN) AF: 0.594 AC: 6257 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35172 AN: 67938

Other (OTH) AF: 0.499 AC: 1051 AN: 2108

Alfa AF: 0.416 Hom.: 2564

Bravo AF: 0.493

Asia WGS AF: 0.632 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.17
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1905261; hg19: chr4-156502278;