7-49550951-T-C

Position:

• chr7-49550951-T-C

Variant summary

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

The ENST00000664348.1(ENSG00000286995):​n.128+26616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,060 control chromosomes in the GnomAD database, including 8,597 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 0.32 (8597 hom., cov: 32)
• Consequence: ENSG00000286995 ENST00000664348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

ENSG00000286995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901804	XR_007060628.1	n.126+26616T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286995	ENST00000664348.1	n.128+26616T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47914 AN: 151942 Hom.: 8587 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.315 AC: 47960 AN: 152060 Hom.: 8597 Cov.: 32 AF XY: 0.323 AC XY: 24016 AN XY: 74318

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.329

Alfa AF: 0.265 Hom.: 987

Bravo AF: 0.303

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2107699; hg19: chr7-49590547;