chr3-61428140-C-G

Variant names:

• chr3-61428140-C-G
• rs10514718
• ENST00000836317.1:n.142+374G>C

Variant summary

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

The ENST00000836317.1(ENSG00000308777):​n.142+374G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,114 control chromosomes in the GnomAD database, including 425 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 0.067 (425 hom., cov: 31)
• Consequence: ENSG00000308777 ENST00000836317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 13 publications found

Genes affected

ENSG00000308777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377114	XR_001740725.2	n.202+374G>C		intron_variant	Intron 1 of 5
LOC105377114	XR_940892.3	n.202+374G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308777	ENST00000836317.1	n.142+374G>C		intron_variant	Intron 2 of 5
ENSG00000308777	ENST00000836318.1	n.128+374G>C		intron_variant	Intron 1 of 4
ENSG00000308777	ENST00000836319.1	n.128+374G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10142 AN: 151996 Hom.: 424 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.0599

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0668 AC: 10165 AN: 152114 Hom.: 425 Cov.: 31 AF XY: 0.0706 AC XY: 5248 AN XY: 74350

African (AFR) AF: 0.0850 AC: 3526 AN: 41476

American (AMR) AF: 0.0686 AC: 1047 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3466

East Asian (EAS) AF: 0.0602 AC: 311 AN: 5166

South Asian (SAS) AF: 0.141 AC: 679 AN: 4816

European-Finnish (FIN) AF: 0.0912 AC: 964 AN: 10574

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3277 AN: 68028

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0520 Hom.: 147

Bravo AF: 0.0646

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10514718; hg19: chr3-61413814;