5-61551192-T-C

Variant names:

• chr5-61551192-T-C
• rs1550816

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 0.457 in 152,124 control chromosomes in the GnomAD database, including 16,153 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 0.46 (16153 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 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: 0.457 AC: 69486 AN: 152006 Hom.: 16144 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.457 AC: 69547 AN: 152124 Hom.: 16153 Cov.: 33 AF XY: 0.460 AC XY: 34236 AN XY: 74370

African (AFR) AF: 0.483 AC: 20060 AN: 41506

American (AMR) AF: 0.506 AC: 7735 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1746 AN: 3466

East Asian (EAS) AF: 0.491 AC: 2540 AN: 5174

South Asian (SAS) AF: 0.610 AC: 2945 AN: 4830

European-Finnish (FIN) AF: 0.400 AC: 4223 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28868 AN: 67982

Other (OTH) AF: 0.456 AC: 964 AN: 2114

Alfa AF: 0.442 Hom.: 25711

Bravo AF: 0.461

Asia WGS AF: 0.573 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.46
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1550816; hg19: chr5-60847019; COSMIC: COSV60140744;