rs7241996

Variant names:

• chr18-37910251-T-C
• rs7241996

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 0.244 in 151,844 control chromosomes in the GnomAD database, including 4,980 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 0.24 (4980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.38 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: 0.244 AC: 36994 AN: 151726 Hom.: 4979 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.244 AC: 37005 AN: 151844 Hom.: 4980 Cov.: 31 AF XY: 0.243 AC XY: 18052 AN XY: 74204

African (AFR) AF: 0.148 AC: 6141 AN: 41440

American (AMR) AF: 0.388 AC: 5905 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3470

East Asian (EAS) AF: 0.186 AC: 956 AN: 5150

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4818

European-Finnish (FIN) AF: 0.273 AC: 2879 AN: 10532

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18430 AN: 67894

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.268 Hom.: 1051

Bravo AF: 0.249

Asia WGS AF: 0.205 AC: 712 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	3.4
DANN	Benign	0.72
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7241996; hg19: chr18-35490215;