5-103068317-A-G

Variant names:

• chr5-103068317-A-G
• rs34374
• XR_948633.2:n.277+767T>C

Variant summary

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

The XR_948633.2(LOC105379105):​n.277+767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,146 control chromosomes in the GnomAD database, including 17,048 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 0.45 (17048 hom., cov: 33)
• Consequence: LOC105379105 XR_948633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 8 publications found

Genes affected

LOC105379105 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379105	XR_948633.2	n.277+767T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68519 AN: 152028 Hom.: 16998 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.451 AC: 68627 AN: 152146 Hom.: 17048 Cov.: 33 AF XY: 0.446 AC XY: 33187 AN XY: 74394

African (AFR) AF: 0.670 AC: 27807 AN: 41496

American (AMR) AF: 0.417 AC: 6372 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2586 AN: 5180

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4822

European-Finnish (FIN) AF: 0.344 AC: 3641 AN: 10590

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24599 AN: 67990

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.382 Hom.: 6783

Bravo AF: 0.467

Asia WGS AF: 0.384 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs34374; hg19: chr5-102404021; COSMIC: COSV60175258;