rs74992754

Variant names:

• chr6-31100249-C-A
• rs74992754

Your query was ambiguous. Multiple possible variants found:

• chr6-31100249-C-A
• chr6-31100249-C-T

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 0.16 in 152,118 control chromosomes in the GnomAD database, including 2,212 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 0.16 (2212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.160 AC: 24272 AN: 152000 Hom.: 2215 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.160 AC: 24282 AN: 152118 Hom.: 2212 Cov.: 32 AF XY: 0.161 AC XY: 11955 AN XY: 74356

African (AFR) AF: 0.102 AC: 4244 AN: 41488

American (AMR) AF: 0.163 AC: 2498 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 487 AN: 3464

East Asian (EAS) AF: 0.373 AC: 1929 AN: 5174

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1475 AN: 10592

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11800 AN: 67990

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.166 Hom.: 3442

Bravo AF: 0.155

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs74992754; hg19: chr6-31068026;