rs11204538

Variant names:

• chr1-247882970-C-T
• rs11204538

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 0.549 in 151,976 control chromosomes in the GnomAD database, including 23,075 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 0.55 (23075 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 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: 0.549 AC: 83313 AN: 151858 Hom.: 23056 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.549 AC: 83377 AN: 151976 Hom.: 23075 Cov.: 33 AF XY: 0.551 AC XY: 40910 AN XY: 74280

African (AFR) AF: 0.585 AC: 24246 AN: 41430

American (AMR) AF: 0.508 AC: 7751 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1715 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3987 AN: 5176

South Asian (SAS) AF: 0.581 AC: 2800 AN: 4816

European-Finnish (FIN) AF: 0.557 AC: 5874 AN: 10542

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35282 AN: 67958

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.534 Hom.: 101424

Bravo AF: 0.549

Asia WGS AF: 0.716 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.51
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11204538; hg19: chr1-248046272;