5-165950694-G-C

Position:

• chr5-165950694-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.00716

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.00697

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.103

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9313296; hg19: chr5-165377699;