ENST00000762170.1:n.98-195A>G

Variant names:

• chr6-95765839-A-G
• rs4645429
• ENST00000762170.1:n.98-195A>G

Variant summary

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

The ENST00000762170.1(ENSG00000299276):​n.98-195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,192 control chromosomes in the GnomAD database, including 394 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 0.059 (394 hom., cov: 32)
• Consequence: ENSG00000299276 ENST00000762170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 2 publications found

Genes affected

ENSG00000299276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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
ENSG00000299276	ENST00000762170.1	n.98-195A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9032 AN: 152076 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0594 AC: 9040 AN: 152192 Hom.: 394 Cov.: 32 AF XY: 0.0624 AC XY: 4644 AN XY: 74400

African (AFR) AF: 0.0323 AC: 1340 AN: 41550

American (AMR) AF: 0.0822 AC: 1255 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1112 AN: 5142

South Asian (SAS) AF: 0.113 AC: 543 AN: 4826

European-Finnish (FIN) AF: 0.0779 AC: 826 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3589 AN: 68016

Other (OTH) AF: 0.0597 AC: 126 AN: 2110

Alfa AF: 0.0535 Hom.: 44

Bravo AF: 0.0575

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs4645429; hg19: chr6-96213715;