rs4430957

Variant names:

• chr2-214604270-G-A
• rs4430957
• ENST00000412896.5:n.177+78812C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-214604270-G-A
• chr2-214604270-G-C
• chr2-214604270-G-T

Variant summary

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

The ENST00000412896.5(ENSG00000197585):​n.177+78812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 150,818 control chromosomes in the GnomAD database, including 47,925 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 0.79 (47925 hom., cov: 25)
• Consequence: ENSG00000197585 ENST00000412896.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 4 publications found

Genes affected

ENSG00000197585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.85 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
ENSG00000197585	ENST00000412896.5	n.177+78812C>T		intron_variant	Intron 2 of 3	4
ENSG00000197585	ENST00000437883.1	n.132+79845C>T		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.791 AC: 119274 AN: 150700 Hom.: 47892 Cov.: 25

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.791 AC: 119360 AN: 150818 Hom.: 47925 Cov.: 25 AF XY: 0.793 AC XY: 58376 AN XY: 73604

African (AFR) AF: 0.639 AC: 26210 AN: 41030

American (AMR) AF: 0.841 AC: 12741 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2874 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4103 AN: 5108

South Asian (SAS) AF: 0.842 AC: 3964 AN: 4706

European-Finnish (FIN) AF: 0.854 AC: 8847 AN: 10360

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.856 AC: 57928 AN: 67704

Other (OTH) AF: 0.800 AC: 1666 AN: 2082

Alfa AF: 0.823 Hom.: 8739

Bravo AF: 0.782

Asia WGS AF: 0.822 AC: 2858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.38
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs4430957; hg19: chr2-215468994;