chr10-120979038-G-T

Variant names:

• chr10-120979038-G-T
• rs11199686
• ENST00000414774.1:n.49+1614C>A

Variant summary

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

The ENST00000414774.1(ENSG00000227307):​n.49+1614C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,006 control chromosomes in the GnomAD database, including 11,991 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 0.39 (11991 hom., cov: 33)
• Consequence: ENSG00000227307 ENST00000414774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.15
• Publications: 1 publications found

Genes affected

ENSG00000227307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227307	ENST00000414774.1	TSL:3	n.49+1614C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58824 AN: 151888 Hom.: 11989 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.387 AC: 58855 AN: 152006 Hom.: 11991 Cov.: 33 AF XY: 0.383 AC XY: 28453 AN XY: 74312

African (AFR) AF: 0.274 AC: 11345 AN: 41478

American (AMR) AF: 0.438 AC: 6690 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1387 AN: 3460

East Asian (EAS) AF: 0.268 AC: 1382 AN: 5150

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4218 AN: 10560

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31019 AN: 67952

Other (OTH) AF: 0.384 AC: 808 AN: 2106

Alfa AF: 0.389 Hom.: 6484

Bravo AF: 0.389

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.56
PhyloP100		-5.2

Splicing

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

Other links and lift over

dbSNP: rs11199686; hg19: chr10-122738551;