rs3761248

Variant names:

• chr20-3069747-T-C
• rs3761248
• ENST00000812739.1:n.89-333A>G

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.89-333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,292 control chromosomes in the GnomAD database, including 1,723 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 0.14 (1723 hom., cov: 33)
• Consequence: ENSG00000305741 ENST00000812739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 17 publications found

Genes affected

ENSG00000305741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.69-333A>G		intron_variant	Intron 1 of 1
LOC101929098	XR_430278.4	n.104-333A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305741	ENST00000812739.1	n.89-333A>G		intron_variant	Intron 1 of 1
ENSG00000305741	ENST00000812740.1	n.300-333A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21789 AN: 152174 Hom.: 1721 Cov.: 33

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.143 AC: 21798 AN: 152292 Hom.: 1723 Cov.: 33 AF XY: 0.142 AC XY: 10603 AN XY: 74450

African (AFR) AF: 0.0963 AC: 4003 AN: 41572

American (AMR) AF: 0.123 AC: 1882 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.161 AC: 833 AN: 5180

South Asian (SAS) AF: 0.163 AC: 787 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1429 AN: 10618

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11435 AN: 68016

Other (OTH) AF: 0.178 AC: 377 AN: 2116

Alfa AF: 0.156 Hom.: 3300

Bravo AF: 0.140

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.83
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs3761248; hg19: chr20-3050393;