rs10896438

Variant names:

• chr11-69139102-T-G
• rs10896438
• ENST00000637084.1:n.*511+3570T>G

Variant summary

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

The ENST00000637084.1(ENSG00000287725):​n.*511+3570T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,960 control chromosomes in the GnomAD database, including 6,479 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 0.29 (6479 hom., cov: 32)
• Consequence: ENSG00000287725 ENST00000637084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 15 publications found

Genes affected

ENSG00000287725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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
ENSG00000287725	ENST00000637084.1	n.*511+3570T>G		intron_variant	Intron 14 of 14	1		ENSP00000490615.1
ENSG00000287725	ENST00000692585.1	n.*511+3570T>G		intron_variant	Intron 14 of 14			ENSP00000509200.1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43609 AN: 151842 Hom.: 6464 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.287 AC: 43669 AN: 151960 Hom.: 6479 Cov.: 32 AF XY: 0.287 AC XY: 21314 AN XY: 74278

African (AFR) AF: 0.253 AC: 10477 AN: 41420

American (AMR) AF: 0.274 AC: 4175 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1686 AN: 5170

South Asian (SAS) AF: 0.176 AC: 850 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3406 AN: 10540

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21089 AN: 67964

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.302 Hom.: 14545

Bravo AF: 0.287

Asia WGS AF: 0.302 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.23
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10896438; hg19: chr11-68906570;