rs1348276

Variant names:

• chr4-99404473-A-C
• rs1348276
• ENST00000762196.1:n.116T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-99404473-A-C
• chr4-99404473-A-G
• chr4-99404473-A-T

Variant summary

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

The ENST00000762196.1(ENSG00000299279):​n.116T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,934 control chromosomes in the GnomAD database, including 17,125 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 0.46 (17125 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_427569.4	n.908T>G		non_coding_transcript_exon_variant	Exon 1 of 4
LOC102723576	XR_939020.3	n.908T>G		non_coding_transcript_exon_variant	Exon 1 of 5
LOC102723576	XR_001741777.2	n.164-295T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762196.1	n.116T>G		non_coding_transcript_exon_variant	Exon 1 of 5
ENSG00000299279	ENST00000762194.1	n.154-295T>G		intron_variant	Intron 1 of 4
ENSG00000299279	ENST00000762195.1	n.26-295T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69530 AN: 151816 Hom.: 17113 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.458 AC: 69587 AN: 151934 Hom.: 17125 Cov.: 32 AF XY: 0.456 AC XY: 33873 AN XY: 74272

African (AFR) AF: 0.641 AC: 26563 AN: 41416

American (AMR) AF: 0.352 AC: 5369 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3150 AN: 5144

South Asian (SAS) AF: 0.502 AC: 2419 AN: 4822

European-Finnish (FIN) AF: 0.325 AC: 3433 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26272 AN: 67926

Other (OTH) AF: 0.419 AC: 883 AN: 2108

Alfa AF: 0.396 Hom.: 15927

Bravo AF: 0.468

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1348276; hg19: chr4-100325630;