chr11-70199230-C-T

Variant names:

• chr11-70199230-C-T
• rs11604809

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 0.343 in 151,416 control chromosomes in the GnomAD database, including 9,775 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 0.34 (9775 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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: 0.343 AC: 51934 AN: 151298 Hom.: 9768 Cov.: 28

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.343 AC: 51968 AN: 151416 Hom.: 9775 Cov.: 28 AF XY: 0.346 AC XY: 25597 AN XY: 73936

African (AFR) AF: 0.192 AC: 7939 AN: 41290

American (AMR) AF: 0.325 AC: 4940 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1587 AN: 3460

East Asian (EAS) AF: 0.557 AC: 2850 AN: 5114

South Asian (SAS) AF: 0.294 AC: 1404 AN: 4780

European-Finnish (FIN) AF: 0.443 AC: 4623 AN: 10434

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.406 AC: 27550 AN: 67842

Other (OTH) AF: 0.335 AC: 705 AN: 2104

Alfa AF: 0.273 Hom.: 959

Bravo AF: 0.327

Asia WGS AF: 0.404 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11604809; hg19: chr11-70045336;