7-46849893-T-C

Variant names:

• chr7-46849893-T-C
• rs4236383
• ENST00000836277.1:n.213-18419T>C

Variant summary

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

The ENST00000836277.1(ENSG00000308757):​n.213-18419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,090 control chromosomes in the GnomAD database, including 7,566 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 (7566 hom., cov: 32)
• Consequence: ENSG00000308757 ENST00000836277.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 6 publications found

Genes affected

ENSG00000308757 (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 (EAS) allele frequency at 95% confidence interval = 0.447 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
ENSG00000308757	ENST00000836277.1	n.213-18419T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47514 AN: 151972 Hom.: 7570 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.312 AC: 47515 AN: 152090 Hom.: 7566 Cov.: 32 AF XY: 0.313 AC XY: 23236 AN XY: 74352

African (AFR) AF: 0.253 AC: 10517 AN: 41488

American (AMR) AF: 0.329 AC: 5027 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2390 AN: 5170

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3325 AN: 10580

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22500 AN: 67986

Other (OTH) AF: 0.312 AC: 661 AN: 2116

Alfa AF: 0.328 Hom.: 5651

Bravo AF: 0.316

Asia WGS AF: 0.398 AC: 1376 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.67
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4236383; hg19: chr7-46889491;