10-56049270-G-T

Variant names:

• chr10-56049270-G-T
• rs11005196
• ENST00000763494.1:n.197-2928G>T

Variant summary

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

The ENST00000763494.1(ENSG00000299437):​n.197-2928G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 151,712 control chromosomes in the GnomAD database, including 93 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 0.032 (93 hom., cov: 32)
• Consequence: ENSG00000299437 ENST00000763494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 0 publications found

Genes affected

ENSG00000299437 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.0683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763494.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299437	ENST00000763494.1		n.197-2928G>T		intron	N/A
	ENSG00000299437	ENST00000763495.1		n.91-2928G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4825 AN: 151594 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0880

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0318 AC: 4817 AN: 151712 Hom.: 93 Cov.: 32 AF XY: 0.0334 AC XY: 2479 AN XY: 74126

African (AFR) AF: 0.0166 AC: 688 AN: 41398

American (AMR) AF: 0.0363 AC: 553 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0880 AC: 305 AN: 3464

East Asian (EAS) AF: 0.0691 AC: 356 AN: 5154

South Asian (SAS) AF: 0.0747 AC: 359 AN: 4808

European-Finnish (FIN) AF: 0.0388 AC: 409 AN: 10530

Middle Eastern (MID) AF: 0.0655 AC: 19 AN: 290

European-Non Finnish (NFE) AF: 0.0300 AC: 2033 AN: 67840

Other (OTH) AF: 0.0433 AC: 91 AN: 2104

Alfa AF: 0.0299 Hom.: 56

Bravo AF: 0.0318

Asia WGS AF: 0.0540 AC: 186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11005196; hg19: chr10-57809031;