rs1145724

Variant names:

• chr6-90477791-T-C
• rs1145724
• ENST00000741973.1:n.217-396T>C

Variant summary

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

The ENST00000741973.1(ENSG00000296783):​n.217-396T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,144 control chromosomes in the GnomAD database, including 8,370 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 0.26 (8370 hom., cov: 33)
• Consequence: ENSG00000296783 ENST00000741973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 4 publications found

Genes affected

ENSG00000296783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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
ENSG00000296783	ENST00000741973.1	n.217-396T>C		intron_variant	Intron 2 of 2
ENSG00000296783	ENST00000741975.1	n.371-396T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39587 AN: 152026 Hom.: 8361 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.260 AC: 39630 AN: 152144 Hom.: 8370 Cov.: 33 AF XY: 0.257 AC XY: 19120 AN XY: 74424

African (AFR) AF: 0.584 AC: 24217 AN: 41444

American (AMR) AF: 0.159 AC: 2432 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5184

South Asian (SAS) AF: 0.127 AC: 614 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1714 AN: 10594

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9248 AN: 68010

Other (OTH) AF: 0.246 AC: 520 AN: 2114

Alfa AF: 0.171 Hom.: 14057

Bravo AF: 0.272

Asia WGS AF: 0.134 AC: 467 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	3.6
DANN	Benign	0.75
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1145724; hg19: chr6-91187510;