7-27105302-C-T

Variant names:

• chr7-27105302-C-T
• rs1725074
• ENST00000716605.1:n.310+8914C>T

Variant summary

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

The ENST00000716605.1(ENSG00000293629):​n.310+8914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,994 control chromosomes in the GnomAD database, including 5,639 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 0.23 (5639 hom., cov: 32)
• Consequence: ENSG00000293629 ENST00000716605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 11 publications found

Genes affected

ENSG00000293629 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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
ENSG00000293629	ENST00000716605.1	n.310+8914C>T		intron_variant	Intron 1 of 1
ENSG00000293629	ENST00000716620.1	n.278+8914C>T		intron_variant	Intron 1 of 2
ENSG00000302880	ENST00000790210.1	n.182-7181G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35464 AN: 151876 Hom.: 5613 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.234 AC: 35537 AN: 151994 Hom.: 5639 Cov.: 32 AF XY: 0.233 AC XY: 17277 AN XY: 74294

African (AFR) AF: 0.447 AC: 18519 AN: 41396

American (AMR) AF: 0.253 AC: 3867 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3466

East Asian (EAS) AF: 0.154 AC: 794 AN: 5170

South Asian (SAS) AF: 0.130 AC: 628 AN: 4824

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9148 AN: 67974

Other (OTH) AF: 0.216 AC: 455 AN: 2108

Alfa AF: 0.194 Hom.: 2646

Bravo AF: 0.256

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.6
DANN	Benign	0.69
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1725074; hg19: chr7-27144921;