chr5-66244019-T-C

Variant names:

• chr5-66244019-T-C
• rs29456

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 0.72 in 152,146 control chromosomes in the GnomAD database, including 40,429 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 0.72 (40429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.771 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: 0.720 AC: 109531 AN: 152026 Hom.: 40407 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.720 AC: 109593 AN: 152146 Hom.: 40429 Cov.: 32 AF XY: 0.712 AC XY: 52947 AN XY: 74372

African (AFR) AF: 0.714 AC: 29639 AN: 41512

American (AMR) AF: 0.637 AC: 9733 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1413 AN: 5146

South Asian (SAS) AF: 0.536 AC: 2588 AN: 4824

European-Finnish (FIN) AF: 0.751 AC: 7956 AN: 10594

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52833 AN: 67994

Other (OTH) AF: 0.732 AC: 1544 AN: 2110

Alfa AF: 0.759 Hom.: 73994

Bravo AF: 0.712

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs29456; hg19: chr5-65539847;