rs749100

Variant names:

• chr5-64012035-A-G
• rs749100

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 0.426 in 151,950 control chromosomes in the GnomAD database, including 14,489 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 0.43 (14489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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: 0.426 AC: 64745 AN: 151830 Hom.: 14466 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.426 AC: 64806 AN: 151950 Hom.: 14489 Cov.: 32 AF XY: 0.418 AC XY: 31025 AN XY: 74272

African (AFR) AF: 0.545 AC: 22587 AN: 41444

American (AMR) AF: 0.392 AC: 5968 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3466

East Asian (EAS) AF: 0.149 AC: 770 AN: 5164

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3120 AN: 10576

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27587 AN: 67930

Other (OTH) AF: 0.427 AC: 903 AN: 2114

Alfa AF: 0.414 Hom.: 1666

Bravo AF: 0.441

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs749100; hg19: chr5-63307862;