chr7-41428348-A-G

Variant names:

• chr7-41428348-A-G
• rs4141153
• ENST00000813847.1:n.278-7163T>C

Variant summary

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

The ENST00000813847.1(ENSG00000305895):​n.278-7163T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,086 control chromosomes in the GnomAD database, including 3,479 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 0.21 (3479 hom., cov: 32)
• Consequence: ENSG00000305895 ENST00000813847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 10 publications found

Genes affected

ENSG00000305895 (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 (AFR) allele frequency at 95% confidence interval = 0.239 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
ENSG00000305895	ENST00000813847.1	n.278-7163T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31916 AN: 151966 Hom.: 3470 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.210 AC: 31947 AN: 152086 Hom.: 3479 Cov.: 32 AF XY: 0.210 AC XY: 15624 AN XY: 74338

African (AFR) AF: 0.243 AC: 10073 AN: 41484

American (AMR) AF: 0.152 AC: 2330 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5164

South Asian (SAS) AF: 0.162 AC: 782 AN: 4816

European-Finnish (FIN) AF: 0.260 AC: 2747 AN: 10582

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13388 AN: 67970

Other (OTH) AF: 0.194 AC: 411 AN: 2114

Alfa AF: 0.201 Hom.: 2917

Bravo AF: 0.202

Asia WGS AF: 0.167 AC: 580 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	4.9
DANN	Benign	0.90
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4141153; hg19: chr7-41467946;