rs43041

Variant names:

• chr7-95441526-C-A
• rs43041
• ENST00000818771.1:n.639+5921C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-95441526-C-A
• chr7-95441526-C-T

Variant summary

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

The ENST00000818771.1(ENSG00000233942):​n.639+5921C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,086 control chromosomes in the GnomAD database, including 51,769 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 0.82 (51769 hom., cov: 30)
• Consequence: ENSG00000233942 ENST00000818771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 10 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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
ENSG00000233942	ENST00000818771.1	n.639+5921C>A		intron_variant	Intron 2 of 8
ENSG00000233942	ENST00000818772.1	n.464-29166C>A		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1	n.553+5921C>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125236 AN: 151968 Hom.: 51727 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.824 AC: 125332 AN: 152086 Hom.: 51769 Cov.: 30 AF XY: 0.825 AC XY: 61299 AN XY: 74322

African (AFR) AF: 0.817 AC: 33890 AN: 41476

American (AMR) AF: 0.826 AC: 12630 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4947 AN: 5160

South Asian (SAS) AF: 0.881 AC: 4241 AN: 4812

European-Finnish (FIN) AF: 0.830 AC: 8783 AN: 10580

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55734 AN: 67980

Other (OTH) AF: 0.802 AC: 1693 AN: 2112

Alfa AF: 0.815 Hom.: 212920

Bravo AF: 0.819

Asia WGS AF: 0.909 AC: 3163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.37
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs43041; hg19: chr7-95070838;