rs1424548

Variant names:

• chr7-137025013-C-T
• rs1424548
• ENST00000439694.6:n.655+6892G>A

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+6892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,806 control chromosomes in the GnomAD database, including 8,297 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 0.32 (8297 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 7 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+7781G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+6892G>A		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+7781G>A		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+7781G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48556 AN: 151690 Hom.: 8289 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0132

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.320 AC: 48586 AN: 151806 Hom.: 8297 Cov.: 32 AF XY: 0.316 AC XY: 23423 AN XY: 74150

African (AFR) AF: 0.254 AC: 10524 AN: 41442

American (AMR) AF: 0.275 AC: 4190 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1183 AN: 3462

East Asian (EAS) AF: 0.0134 AC: 69 AN: 5134

South Asian (SAS) AF: 0.179 AC: 860 AN: 4816

European-Finnish (FIN) AF: 0.394 AC: 4154 AN: 10536

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26419 AN: 67890

Other (OTH) AF: 0.336 AC: 708 AN: 2106

Alfa AF: 0.341 Hom.: 1537

Bravo AF: 0.311

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1424548; hg19: chr7-136709760;