chr5-7244378-A-G

Variant names:

• chr5-7244378-A-G
• rs4276378
• ENST00000835169.1:n.123+6261T>C

Variant summary

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

The ENST00000835169.1(ENSG00000308577):​n.123+6261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,992 control chromosomes in the GnomAD database, including 12,507 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 0.40 (12507 hom., cov: 32)
• Consequence: ENSG00000308577 ENST00000835169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 5 publications found

Genes affected

ENSG00000308577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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
ENSG00000308577	ENST00000835169.1	n.123+6261T>C		intron_variant	Intron 1 of 2
ENSG00000308577	ENST00000835170.1	n.96+6261T>C		intron_variant	Intron 1 of 2
ENSG00000308577	ENST00000835171.1	n.94+6261T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60422 AN: 151872 Hom.: 12495 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.398 AC: 60461 AN: 151992 Hom.: 12507 Cov.: 32 AF XY: 0.404 AC XY: 30017 AN XY: 74278

African (AFR) AF: 0.295 AC: 12240 AN: 41444

American (AMR) AF: 0.424 AC: 6472 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3472

East Asian (EAS) AF: 0.583 AC: 2997 AN: 5142

South Asian (SAS) AF: 0.520 AC: 2498 AN: 4802

European-Finnish (FIN) AF: 0.441 AC: 4660 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28335 AN: 67972

Other (OTH) AF: 0.438 AC: 925 AN: 2112

Alfa AF: 0.409 Hom.: 48123

Bravo AF: 0.390

Asia WGS AF: 0.564 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.039
DANN	Benign	0.51
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4276378; hg19: chr5-7244491;