rs7787362

Variant names:

• chr7-73978273-T-C
• rs7787362
• ENST00000728270.1:n.276-21629T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-73978273-T-C
• chr7-73978273-T-G

Variant summary

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

The ENST00000728270.1(ENSG00000261467):​n.276-21629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,152 control chromosomes in the GnomAD database, including 13,928 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 0.39 (13928 hom., cov: 33)
• Consequence: ENSG00000261467 ENST00000728270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 9 publications found

Genes affected

ENSG00000261467 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 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
ENSG00000261467	ENST00000728270.1	n.276-21629T>C		intron_variant	Intron 1 of 1
ENSG00000261467	ENST00000728271.1	n.230-21629T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60052 AN: 152034 Hom.: 13917 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.395 AC: 60081 AN: 152152 Hom.: 13928 Cov.: 33 AF XY: 0.388 AC XY: 28885 AN XY: 74376

African (AFR) AF: 0.165 AC: 6866 AN: 41526

American (AMR) AF: 0.393 AC: 6011 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1917 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5166

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4822

European-Finnish (FIN) AF: 0.437 AC: 4629 AN: 10588

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36303 AN: 67970

Other (OTH) AF: 0.443 AC: 937 AN: 2114

Alfa AF: 0.477 Hom.: 14018

Bravo AF: 0.377

Asia WGS AF: 0.332 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.027
DANN	Benign	0.51
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7787362; hg19: chr7-73392603;