7-91610982-C-T

Variant names:

• chr7-91610982-C-T
• rs2540552
• ENST00000718159.1:n.97+32392G>A

Variant summary

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

The ENST00000718159.1(ENSG00000223665):​n.97+32392G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,104 control chromosomes in the GnomAD database, including 26,475 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 0.55 (26475 hom., cov: 33)
• Consequence: ENSG00000223665 ENST00000718159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 3 publications found

Genes affected

ENSG00000223665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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
ENSG00000223665	ENST00000718159.1	n.97+32392G>A		intron_variant	Intron 1 of 6
ENSG00000223665	ENST00000718160.1	n.216-27597G>A		intron_variant	Intron 1 of 6
ENSG00000223665	ENST00000718161.1	n.61+32392G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83993 AN: 151988 Hom.: 26425 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.553 AC: 84095 AN: 152104 Hom.: 26475 Cov.: 33 AF XY: 0.555 AC XY: 41242 AN XY: 74334

African (AFR) AF: 0.854 AC: 35469 AN: 41524

American (AMR) AF: 0.504 AC: 7709 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1537 AN: 3468

East Asian (EAS) AF: 0.821 AC: 4254 AN: 5184

South Asian (SAS) AF: 0.600 AC: 2888 AN: 4812

European-Finnish (FIN) AF: 0.397 AC: 4190 AN: 10552

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26543 AN: 67958

Other (OTH) AF: 0.544 AC: 1150 AN: 2114

Alfa AF: 0.487 Hom.: 21362

Bravo AF: 0.574

Asia WGS AF: 0.694 AC: 2410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.30
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2540552; hg19: chr7-91240297;