rs2527894

Positions:

• chr7-99941218-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456499.1(ENSG00000237640):​n.328-2757A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,124 control chromosomes in the GnomAD database, including 32,690 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 0.64 (32690 hom., cov: 33)
• Consequence: ENST00000456499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000456499.1	n.328-2757A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97110 AN: 152006 Hom.: 32640 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.639 AC: 97215 AN: 152124 Hom.: 32690 Cov.: 33 AF XY: 0.634 AC XY: 47112 AN XY: 74352

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.598

Alfa AF: 0.645 Hom.: 6275

Bravo AF: 0.640

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2527894; hg19: chr7-99538841;