chr5-67197252-C-T

Variant names:

• chr5-67197252-C-T
• rs3756561

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 0.195 in 152,126 control chromosomes in the GnomAD database, including 4,952 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 0.19 (4952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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: 0.194 AC: 29554 AN: 152008 Hom.: 4934 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.195 AC: 29628 AN: 152126 Hom.: 4952 Cov.: 32 AF XY: 0.196 AC XY: 14614 AN XY: 74384

African (AFR) AF: 0.455 AC: 18855 AN: 41466

American (AMR) AF: 0.145 AC: 2216 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0583 AC: 202 AN: 3462

East Asian (EAS) AF: 0.186 AC: 966 AN: 5186

South Asian (SAS) AF: 0.166 AC: 800 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4558 AN: 67990

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.113 Hom.: 2077

Bravo AF: 0.203

Asia WGS AF: 0.220 AC: 764 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	6.6
DANN	Benign	0.61
PhyloP100		0.81
PromoterAI		0.0086	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3756561; hg19: chr5-66493080;