rs10972356

Variant names:

• chr9-35153438-A-G
• rs10972356
• ENST00000836210.1:n.423-1835T>C

Variant summary

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

The ENST00000836210.1(ENSG00000308740):​n.423-1835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 139,374 control chromosomes in the GnomAD database, including 8,007 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 0.31 (8007 hom., cov: 21)
• Consequence: ENSG00000308740 ENST00000836210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 3 publications found

Genes affected

ENSG00000308740 (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 (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902147	XR_007061468.1	n.340-1835T>C		intron_variant	Intron 1 of 1
LOC124902147	XR_007061469.1	n.340-1839T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308740	ENST00000836210.1	n.423-1835T>C		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836211.1	n.723-1835T>C		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836212.1	n.963-1835T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.310 AC: 43232 AN: 139340 Hom.: 8001 Cov.: 21

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.310 AC: 43240 AN: 139374 Hom.: 8007 Cov.: 21 AF XY: 0.305 AC XY: 20450 AN XY: 67050

African (AFR) AF: 0.130 AC: 4712 AN: 36108

American (AMR) AF: 0.407 AC: 5494 AN: 13504

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1197 AN: 3408

East Asian (EAS) AF: 0.00579 AC: 28 AN: 4834

South Asian (SAS) AF: 0.179 AC: 787 AN: 4408

European-Finnish (FIN) AF: 0.430 AC: 3469 AN: 8064

Middle Eastern (MID) AF: 0.379 AC: 100 AN: 264

European-Non Finnish (NFE) AF: 0.401 AC: 26497 AN: 66000

Other (OTH) AF: 0.328 AC: 623 AN: 1898

Alfa AF: 0.325 Hom.: 1378

Bravo AF: 0.295

Asia WGS AF: 0.110 AC: 381 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10972356; hg19: chr9-35153435;