rs11977828

Variant names:

• chr7-12255853-A-T
• rs11977828

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 0.337 in 151,954 control chromosomes in the GnomAD database, including 10,832 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 0.34 (10832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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: 0.336 AC: 51068 AN: 151836 Hom.: 10815 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.337 AC: 51134 AN: 151954 Hom.: 10832 Cov.: 32 AF XY: 0.334 AC XY: 24787 AN XY: 74272

African (AFR) AF: 0.604 AC: 24994 AN: 41414

American (AMR) AF: 0.198 AC: 3027 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3462

East Asian (EAS) AF: 0.156 AC: 807 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4824

European-Finnish (FIN) AF: 0.280 AC: 2960 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16489 AN: 67956

Other (OTH) AF: 0.311 AC: 656 AN: 2106

Alfa AF: 0.290 Hom.: 1015

Bravo AF: 0.342

Asia WGS AF: 0.247 AC: 853 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.72
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11977828; hg19: chr7-12295479;