rs7277536

Variant names:

• chr21-28401274-G-A
• rs7277536
• ENST00000657148.1:n.1645+15801C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000657148.1(ENSG00000232855):​n.1645+15801C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00741 in 152,238 control chromosomes in the GnomAD database, including 10 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 0.0074 (10 hom., cov: 33)
• Consequence: ENSG00000232855 ENST00000657148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 1 publications found

Genes affected

ENSG00000232855 (HGNC:58104):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS2: High Homozygotes in GnomAd4 at 10 gene

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
ENSG00000232855	ENST00000657148.1	n.1645+15801C>T		intron_variant	Intron 4 of 4
ENSG00000232855	ENST00000824757.1	n.769+15801C>T		intron_variant	Intron 6 of 8
ENSG00000232855	ENST00000824758.1	n.1180+15801C>T		intron_variant	Intron 9 of 11
ENSG00000232855	ENST00000824759.1	n.851+15801C>T		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.00742 AC: 1128 AN: 152120 Hom.: 10 Cov.: 33

Gnomad AFR AF: 0.00183

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00484

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00547

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.00526

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

GnomAD4 genome AF: 0.00741 AC: 1128 AN: 152238 Hom.: 10 Cov.: 33 AF XY: 0.00660 AC XY: 491 AN XY: 74444

African (AFR) AF: 0.00183 AC: 76 AN: 41544

American (AMR) AF: 0.00484 AC: 74 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4820

European-Finnish (FIN) AF: 0.00547 AC: 58 AN: 10596

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 872 AN: 68008

Other (OTH) AF: 0.00521 AC: 11 AN: 2112

Alfa AF: 0.0143 Hom.: 3

Bravo AF: 0.00706

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7277536; hg19: chr21-29773595;