7-124369982-T-C

Position:

• chr7-124369982-T-C

Variant summary

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

The ENST00000484322.5(ENSG00000242593):​n.295-6340T>C 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 0.226 in 151,824 control chromosomes in the GnomAD database, including 4,445 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 0.23 (4445 hom., cov: 32)
• Consequence: ENST00000484322.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.289 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
	ENST00000652254.1	n.161-66699T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34263 AN: 151706 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.226 AC: 34265 AN: 151824 Hom.: 4445 Cov.: 32 AF XY: 0.220 AC XY: 16307 AN XY: 74230

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.249

Alfa AF: 0.278 Hom.: 8301

Bravo AF: 0.220

Asia WGS AF: 0.155 AC: 535 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487263; hg19: chr7-124010036;