rs11677416

Variant names:

• chr2-112771663-T-C
• rs11677416
• ENST00000762706.1:n.404+767T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762706.1(ENSG00000299339):​n.404+767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,976 control chromosomes in the GnomAD database, including 5,265 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 0.26 (5265 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 17 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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
ENSG00000299339	ENST00000762706.1	n.404+767T>C		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+767T>C		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+767T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38862 AN: 151858 Hom.: 5261 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.256 AC: 38888 AN: 151976 Hom.: 5265 Cov.: 31 AF XY: 0.258 AC XY: 19155 AN XY: 74266

African (AFR) AF: 0.179 AC: 7432 AN: 41488

American (AMR) AF: 0.269 AC: 4116 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3464

East Asian (EAS) AF: 0.0797 AC: 413 AN: 5182

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3300 AN: 10528

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19982 AN: 67906

Other (OTH) AF: 0.261 AC: 551 AN: 2110

Alfa AF: 0.276 Hom.: 850

Bravo AF: 0.246

Asia WGS AF: 0.201 AC: 699 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11677416; hg19: chr2-113529240;