chr5-165950694-G-C

Variant names:

• chr5-165950694-G-C
• rs9313296

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 0.123 in 152,094 control chromosomes in the GnomAD database, including 3,013 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 0.12 (3013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18653 AN: 151976 Hom.: 2995 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.00715

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00697

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.123 AC: 18711 AN: 152094 Hom.: 3013 Cov.: 32 AF XY: 0.119 AC XY: 8840 AN XY: 74360

African (AFR) AF: 0.371 AC: 15369 AN: 41446

American (AMR) AF: 0.0633 AC: 967 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.00716 AC: 37 AN: 5166

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4816

European-Finnish (FIN) AF: 0.00697 AC: 74 AN: 10614

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0257 AC: 1746 AN: 67990

Other (OTH) AF: 0.103 AC: 216 AN: 2106

Alfa AF: 0.0298 Hom.: 129

Bravo AF: 0.141

Asia WGS AF: 0.0480 AC: 166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.35
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9313296; hg19: chr5-165377699;