chr4-99386010-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.388-2390C>T		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1285-2390C>T		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1285-2390C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.378-2390C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762195.1	n.250-2390C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762196.1	n.493-2390C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762197.1	n.250-2390C>T		intron_variant	Intron 3 of 3

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 v4.3

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;