rs11242674

Variant names:

• chr6-1307611-A-G
• rs11242674

Your query was ambiguous. Multiple possible variants found:

• chr6-1307611-A-G
• chr6-1307611-A-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 0.572 in 152,070 control chromosomes in the GnomAD database, including 25,324 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 (25324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 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: 87014 AN: 151952 Hom.: 25313 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.572 AC: 87047 AN: 152070 Hom.: 25324 Cov.: 32 AF XY: 0.570 AC XY: 42360 AN XY: 74330

African (AFR) AF: 0.493 AC: 20444 AN: 41480

American (AMR) AF: 0.477 AC: 7291 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2463 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3421 AN: 5156

South Asian (SAS) AF: 0.607 AC: 2919 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6266 AN: 10580

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42187 AN: 67970

Other (OTH) AF: 0.577 AC: 1218 AN: 2112

Alfa AF: 0.602 Hom.: 75393

Bravo AF: 0.559

Asia WGS AF: 0.641 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11242674; hg19: chr6-1307846;