rs11085374

Variant names:

• chr19-20723414-T-A
• rs11085374

Your query was ambiguous. Multiple possible variants found:

• chr19-20723414-T-A
• chr19-20723414-T-C
• chr19-20723414-T-G

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 0.352 in 151,898 control chromosomes in the GnomAD database, including 10,323 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 0.35 (10323 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.352 AC: 53451 AN: 151778 Hom.: 10297 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.352 AC: 53523 AN: 151898 Hom.: 10323 Cov.: 31 AF XY: 0.347 AC XY: 25761 AN XY: 74238

African (AFR) AF: 0.504 AC: 20863 AN: 41398

American (AMR) AF: 0.239 AC: 3650 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3468

East Asian (EAS) AF: 0.177 AC: 914 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4810

European-Finnish (FIN) AF: 0.309 AC: 3251 AN: 10536

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21403 AN: 67936

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.197 Hom.: 395

Bravo AF: 0.355

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.18
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11085374; hg19: chr19-20906220;