7-81777764-T-C

Variant names:

• chr7-81777764-T-C
• rs1558001
• ENST00000771413.1:n.118-2459T>C

Variant summary

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

The ENST00000771413.1(ENSG00000300407):​n.118-2459T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,982 control chromosomes in the GnomAD database, including 31,125 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 0.63 (31125 hom., cov: 32)
• Consequence: ENSG00000300407 ENST00000771413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 4 publications found

Genes affected

ENSG00000300407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771413.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300407	ENST00000771413.1		n.118-2459T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96190 AN: 151864 Hom.: 31087 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.633 AC: 96272 AN: 151982 Hom.: 31125 Cov.: 32 AF XY: 0.631 AC XY: 46876 AN XY: 74262

African (AFR) AF: 0.747 AC: 30985 AN: 41472

American (AMR) AF: 0.565 AC: 8616 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2541 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2934 AN: 5166

South Asian (SAS) AF: 0.743 AC: 3578 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5686 AN: 10540

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39920 AN: 67952

Other (OTH) AF: 0.635 AC: 1341 AN: 2112

Alfa AF: 0.608 Hom.: 36484

Bravo AF: 0.639

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.53
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1558001; hg19: chr7-81407080;