rs7146104

Variant names:

• chr14-60622618-G-A
• rs7146104
• ENST00000827601.1:n.407-11525C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000827601.1(ENSG00000307639):​n.407-11525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 152,230 control chromosomes in the GnomAD database, including 44 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 0.014 (44 hom., cov: 33)
• Consequence: ENSG00000307639 ENST00000827601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

ENSG00000307639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0139 (2110/152230) while in subpopulation AFR AF = 0.0488 (2026/41522). AF 95% confidence interval is 0.047. There are 44 homozygotes in GnomAd4. There are 997 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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
ENSG00000307639	ENST00000827601.1	n.407-11525C>T		intron_variant	Intron 2 of 3
ENSG00000307639	ENST00000827602.1	n.404+18945C>T		intron_variant	Intron 2 of 2
ENSG00000307639	ENST00000827603.1	n.401-11525C>T		intron_variant	Intron 2 of 3
ENSG00000307639	ENST00000827604.1	n.681-8446C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0138 AC: 2105 AN: 152112 Hom.: 44 Cov.: 33

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00909

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

GnomAD4 genome AF: 0.0139 AC: 2110 AN: 152230 Hom.: 44 Cov.: 33 AF XY: 0.0134 AC XY: 997 AN XY: 74442

African (AFR) AF: 0.0488 AC: 2026 AN: 41522

American (AMR) AF: 0.00327 AC: 50 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 68024

Other (OTH) AF: 0.00900 AC: 19 AN: 2112

Alfa AF: 0.0113 Hom.: 3

Bravo AF: 0.0156

Asia WGS AF: 0.00231 AC: 8 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	0.48
DANN	Benign	0.15
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7146104; hg19: chr14-61089336;