rs10516441

Variant names:

• chr4-99386010-G-A
• rs10516441
• ENST00000762194.1:n.378-2390C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99386010-G-A
• chr4-99386010-G-C

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.378-2390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 152,110 control chromosomes in the GnomAD database, including 1,676 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 0.079 (1676 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 9 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299279	ENST00000762194.1		n.378-2390C>T		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.250-2390C>T		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.493-2390C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11990 AN: 151992 Hom.: 1678 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.0955

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0788 AC: 11987 AN: 152110 Hom.: 1676 Cov.: 32 AF XY: 0.0883 AC XY: 6562 AN XY: 74346

African (AFR) AF: 0.0128 AC: 533 AN: 41530

American (AMR) AF: 0.0438 AC: 668 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3482 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4814

European-Finnish (FIN) AF: 0.0955 AC: 1009 AN: 10570

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0649 AC: 4411 AN: 67992

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0765 Hom.: 441

Bravo AF: 0.0699

Asia WGS AF: 0.389 AC: 1350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10516441; hg19: chr4-100307167;