5-109327414-G-A

Variant names:

• chr5-109327414-G-A
• rs431669

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 0.21 in 152,104 control chromosomes in the GnomAD database, including 4,333 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 0.21 (4333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.210 AC: 31901 AN: 151986 Hom.: 4327 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.210 AC: 31906 AN: 152104 Hom.: 4333 Cov.: 32 AF XY: 0.217 AC XY: 16136 AN XY: 74342

African (AFR) AF: 0.0660 AC: 2739 AN: 41524

American (AMR) AF: 0.256 AC: 3906 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5156

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2799 AN: 10548

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16026 AN: 67990

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.219 Hom.: 873

Bravo AF: 0.200

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.42
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs431669; hg19: chr5-108663115; COSMIC: COSV72667643;