rs721103

Variant names:

• chr3-98553346-A-T
• rs721103
• ENST00000512905.6:n.*70+8978T>A

Variant summary

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

The ENST00000512905.6(ENSG00000285635):​n.*70+8978T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,104 control chromosomes in the GnomAD database, including 7,482 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 (7482 hom., cov: 32)
• Consequence: ENSG00000285635 ENST00000512905.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 3 publications found

Genes affected

ENSG00000285635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 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
ENSG00000285635	ENST00000512905.6	n.*70+8978T>A		intron_variant	Intron 3 of 3	5		ENSP00000425880.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46914 AN: 151984 Hom.: 7472 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.309 AC: 46942 AN: 152104 Hom.: 7482 Cov.: 32 AF XY: 0.310 AC XY: 23052 AN XY: 74352

African (AFR) AF: 0.253 AC: 10492 AN: 41510

American (AMR) AF: 0.263 AC: 4014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5174

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4820

European-Finnish (FIN) AF: 0.345 AC: 3648 AN: 10560

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23439 AN: 67978

Other (OTH) AF: 0.300 AC: 635 AN: 2114

Alfa AF: 0.338 Hom.: 1111

Bravo AF: 0.296

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs721103; hg19: chr3-98272190;