7-36038205-C-T

Variant names:

• chr7-36038205-C-T
• rs10215376
• ENST00000446024.1:n.459+2217C>T

Variant summary

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

The ENST00000446024.1(ENSG00000232930):​n.459+2217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,144 control chromosomes in the GnomAD database, including 7,824 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 (7824 hom., cov: 33)
• Consequence: ENSG00000232930 ENST00000446024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 1 publications found

Genes affected

ENSG00000232930 (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 (SAS) allele frequency at 95% confidence interval = 0.484 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
ENSG00000232930	ENST00000446024.1	n.459+2217C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47242 AN: 152026 Hom.: 7803 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.311 AC: 47320 AN: 152144 Hom.: 7824 Cov.: 33 AF XY: 0.320 AC XY: 23833 AN XY: 74370

African (AFR) AF: 0.309 AC: 12820 AN: 41516

American (AMR) AF: 0.410 AC: 6269 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3472

East Asian (EAS) AF: 0.476 AC: 2465 AN: 5182

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3379 AN: 10566

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18137 AN: 67966

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.283 Hom.: 1134

Bravo AF: 0.315

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10215376; hg19: chr7-36077815;