rs5014418

Variant names:

• chr6-32751604-A-C
• rs5014418

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 0.117 in 152,042 control chromosomes in the GnomAD database, including 1,665 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 (1665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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: 0.117 AC: 17733 AN: 151924 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.00557

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00530

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.117 AC: 17741 AN: 152042 Hom.: 1665 Cov.: 32 AF XY: 0.112 AC XY: 8336 AN XY: 74348

African (AFR) AF: 0.250 AC: 10370 AN: 41398

American (AMR) AF: 0.130 AC: 1987 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0782 AC: 271 AN: 3464

East Asian (EAS) AF: 0.00539 AC: 28 AN: 5196

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4830

European-Finnish (FIN) AF: 0.00530 AC: 56 AN: 10572

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0676 AC: 4592 AN: 67962

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.104 Hom.: 315

Bravo AF: 0.138

Asia WGS AF: 0.0210 AC: 72 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs5014418; hg19: chr6-32719381;