5-91801978-A-G

Variant names:

• chr5-91801978-A-G
• rs2973869

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 0.477 in 151,976 control chromosomes in the GnomAD database, including 17,945 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 0.48 (17945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 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: 0.476 AC: 72338 AN: 151858 Hom.: 17907 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.477 AC: 72428 AN: 151976 Hom.: 17945 Cov.: 32 AF XY: 0.478 AC XY: 35478 AN XY: 74288

African (AFR) AF: 0.603 AC: 24981 AN: 41448

American (AMR) AF: 0.431 AC: 6587 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2990 AN: 5158

South Asian (SAS) AF: 0.590 AC: 2841 AN: 4818

European-Finnish (FIN) AF: 0.387 AC: 4086 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28206 AN: 67930

Other (OTH) AF: 0.438 AC: 925 AN: 2112

Alfa AF: 0.429 Hom.: 3635

Bravo AF: 0.481

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2973869; hg19: chr5-91097795; COSMIC: COSV60167162;