rs9640161

Variant names:

• chr7-150348821-C-A
• rs9640161
• ENST00000782368.1:n.256+5180C>A

Variant summary

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

The ENST00000782368.1(ENSG00000301866):​n.256+5180C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,032 control chromosomes in the GnomAD database, including 11,502 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 0.38 (11502 hom., cov: 33)
• Consequence: ENSG00000301866 ENST00000782368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 11 publications found

Genes affected

ENSG00000301866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986858	XR_001745420.3	n.607+5180C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301866	ENST00000782368.1	n.256+5180C>A		intron_variant	Intron 1 of 1
ENSG00000301866	ENST00000782369.1	n.239+5180C>A		intron_variant	Intron 1 of 1
ENSG00000301866	ENST00000782370.1	n.337+654C>A		intron_variant	Intron 2 of 2
ENSG00000301866	ENST00000782371.1	n.421+558C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58209 AN: 151914 Hom.: 11485 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.383 AC: 58265 AN: 152032 Hom.: 11502 Cov.: 33 AF XY: 0.387 AC XY: 28728 AN XY: 74312

African (AFR) AF: 0.439 AC: 18219 AN: 41466

American (AMR) AF: 0.257 AC: 3928 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2612 AN: 5182

South Asian (SAS) AF: 0.457 AC: 2204 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4483 AN: 10556

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24083 AN: 67946

Other (OTH) AF: 0.349 AC: 735 AN: 2106

Alfa AF: 0.366 Hom.: 5606

Bravo AF: 0.372

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.73
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs9640161; hg19: chr7-150045910;