8-48499856-T-C

Variant names:

• chr8-48499856-T-C
• rs7016759

Variant summary

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

The variant allele was found at a frequency of 0.232 in 152,006 control chromosomes in the GnomAD database, including 4,685 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 (4685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 5 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.344 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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35312 AN: 151888 Hom.: 4678 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.232 AC: 35341 AN: 152006 Hom.: 4685 Cov.: 32 AF XY: 0.231 AC XY: 17195 AN XY: 74332

African (AFR) AF: 0.349 AC: 14438 AN: 41406

American (AMR) AF: 0.210 AC: 3207 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1262 AN: 5142

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4816

European-Finnish (FIN) AF: 0.123 AC: 1303 AN: 10604

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11731 AN: 67970

Other (OTH) AF: 0.255 AC: 538 AN: 2110

Alfa AF: 0.208 Hom.: 479

Bravo AF: 0.244

Asia WGS AF: 0.291 AC: 1011 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	3.8
DANN	Benign	0.61
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs7016759; hg19: chr8-49412416;