rs10065816

Variant names:

• chr5-149646318-G-A
• rs10065816

Your query was ambiguous. Multiple possible variants found:

• chr5-149646318-G-A
• chr5-149646318-G-C

Variant summary

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

The variant allele was found at a frequency of 0.573 in 151,822 control chromosomes in the GnomAD database, including 25,536 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 0.57 (25536 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86971 AN: 151704 Hom.: 25530 Cov.: 30

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.573 AC: 87020 AN: 151822 Hom.: 25536 Cov.: 30 AF XY: 0.575 AC XY: 42665 AN XY: 74156

African (AFR) AF: 0.448 AC: 18542 AN: 41368

American (AMR) AF: 0.496 AC: 7565 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2361 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3511 AN: 5162

South Asian (SAS) AF: 0.555 AC: 2664 AN: 4802

European-Finnish (FIN) AF: 0.691 AC: 7259 AN: 10512

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43074 AN: 67930

Other (OTH) AF: 0.614 AC: 1296 AN: 2110

Alfa AF: 0.597 Hom.: 11799

Bravo AF: 0.551

Asia WGS AF: 0.588 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.23
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10065816; hg19: chr5-149025881;