rs619689

Variant names:

• chr11-114456232-C-G
• rs619689

Your query was ambiguous. Multiple possible variants found:

• chr11-114456232-C-G
• chr11-114456232-C-T

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 0.573 in 151,820 control chromosomes in the GnomAD database, including 25,500 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 0.57 (25500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.573 AC: 86934 AN: 151702 Hom.: 25451 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.573 AC: 87038 AN: 151820 Hom.: 25500 Cov.: 32 AF XY: 0.572 AC XY: 42409 AN XY: 74184

African (AFR) AF: 0.705 AC: 29121 AN: 41308

American (AMR) AF: 0.553 AC: 8452 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3135 AN: 5152

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4818

European-Finnish (FIN) AF: 0.491 AC: 5180 AN: 10552

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34635 AN: 67928

Other (OTH) AF: 0.566 AC: 1192 AN: 2106

Alfa AF: 0.397 Hom.: 1000

Bravo AF: 0.583

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.66
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs619689; hg19: chr11-114326954;