rs638541

Variant names:

• chr9-107959774-T-A
• rs638541
• ENST00000798334.1:n.102-16634A>T

Variant summary

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

The ENST00000798334.1(ENSG00000303954):​n.102-16634A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,146 control chromosomes in the GnomAD database, including 46,411 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 0.78 (46411 hom., cov: 33)
• Consequence: ENSG00000303954 ENST00000798334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 3 publications found

Genes affected

ENSG00000303954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 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
ENSG00000303954	ENST00000798334.1	n.102-16634A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118068 AN: 152028 Hom.: 46388 Cov.: 33

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.776 AC: 118135 AN: 152146 Hom.: 46411 Cov.: 33 AF XY: 0.772 AC XY: 57408 AN XY: 74362

African (AFR) AF: 0.787 AC: 32668 AN: 41502

American (AMR) AF: 0.680 AC: 10388 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2643 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2204 AN: 5162

South Asian (SAS) AF: 0.643 AC: 3096 AN: 4812

European-Finnish (FIN) AF: 0.836 AC: 8869 AN: 10604

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.818 AC: 55647 AN: 68004

Other (OTH) AF: 0.749 AC: 1577 AN: 2106

Alfa AF: 0.812 Hom.: 6293

Bravo AF: 0.763

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs638541; hg19: chr9-110722055;