rs2111701

Variant names:

• chr14-78041455-T-C
• rs2111701

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 0.649 in 151,830 control chromosomes in the GnomAD database, including 32,044 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 0.65 (32044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.666 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: 0.649 AC: 98396 AN: 151712 Hom.: 32024 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.649 AC: 98470 AN: 151830 Hom.: 32044 Cov.: 31 AF XY: 0.642 AC XY: 47630 AN XY: 74148

African (AFR) AF: 0.639 AC: 26462 AN: 41400

American (AMR) AF: 0.671 AC: 10220 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2400 AN: 3472

East Asian (EAS) AF: 0.565 AC: 2915 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2566 AN: 4800

European-Finnish (FIN) AF: 0.585 AC: 6148 AN: 10506

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45603 AN: 67956

Other (OTH) AF: 0.693 AC: 1459 AN: 2106

Alfa AF: 0.668 Hom.: 101652

Bravo AF: 0.657

Asia WGS AF: 0.550 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2111701; hg19: chr14-78507798;