rs11771443

Variant names:

• chr7-150990599-C-T
• rs11771443

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 0.167 in 152,178 control chromosomes in the GnomAD database, including 2,606 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 0.17 (2606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.167 AC: 25365 AN: 152058 Hom.: 2591 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.167 AC: 25402 AN: 152178 Hom.: 2606 Cov.: 32 AF XY: 0.175 AC XY: 13029 AN XY: 74394

African (AFR) AF: 0.0956 AC: 3969 AN: 41528

American (AMR) AF: 0.283 AC: 4334 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2185 AN: 5168

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2176 AN: 10586

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10680 AN: 68002

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.164 Hom.: 2982

Bravo AF: 0.173

Asia WGS AF: 0.341 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.6
DANN	Benign	0.84
PhyloP100		1.1
PromoterAI		0.037	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11771443; hg19: chr7-150687687;