rs11947216

Variant names:

• chr4-178106499-G-A
• rs11947216

Your query was ambiguous. Multiple possible variants found:

• chr4-178106499-G-A
• chr4-178106499-G-C

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 0.308 in 151,950 control chromosomes in the GnomAD database, including 7,456 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 0.31 (7456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.308 AC: 46808 AN: 151832 Hom.: 7453 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.308 AC: 46834 AN: 151950 Hom.: 7456 Cov.: 32 AF XY: 0.307 AC XY: 22848 AN XY: 74306

African (AFR) AF: 0.244 AC: 10124 AN: 41500

American (AMR) AF: 0.264 AC: 4034 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1142 AN: 3464

East Asian (EAS) AF: 0.222 AC: 1144 AN: 5158

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4826

European-Finnish (FIN) AF: 0.341 AC: 3599 AN: 10540

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24245 AN: 67890

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.322 Hom.: 966

Bravo AF: 0.300

Asia WGS AF: 0.258 AC: 895 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.5
DANN	Benign	0.37
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11947216; hg19: chr4-179027653;