rs7531849

Variant names:

• chr1-240731283-A-C
• rs7531849

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 0.0526 in 152,302 control chromosomes in the GnomAD database, including 300 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 0.053 (300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 8003 AN: 152184 Hom.: 299 Cov.: 32

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0526 AC: 8016 AN: 152302 Hom.: 300 Cov.: 32 AF XY: 0.0516 AC XY: 3843 AN XY: 74478

African (AFR) AF: 0.0945 AC: 3928 AN: 41556

American (AMR) AF: 0.0532 AC: 814 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.0776 AC: 402 AN: 5180

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4830

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2325 AN: 68028

Other (OTH) AF: 0.0416 AC: 88 AN: 2116

Alfa AF: 0.0387 Hom.: 461

Bravo AF: 0.0576

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7531849; hg19: chr1-240894583;