rs11904110

Variant names:

• chr2-97645339-T-C
• rs11904110

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 0.135 in 152,208 control chromosomes in the GnomAD database, including 2,269 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 0.14 (2269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.135 AC: 20594 AN: 152090 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.135 AC: 20612 AN: 152208 Hom.: 2269 Cov.: 32 AF XY: 0.131 AC XY: 9741 AN XY: 74434

African (AFR) AF: 0.300 AC: 12438 AN: 41504

American (AMR) AF: 0.102 AC: 1554 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5182

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4828

European-Finnish (FIN) AF: 0.0207 AC: 220 AN: 10616

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5061 AN: 68004

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.0968 Hom.: 3915

Bravo AF: 0.150

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11904110; hg19: chr2-98261802;