chr4-105536173-T-C

Variant names:

• chr4-105536173-T-C
• rs7669317
• NR_188418.1:n.1742A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_188418.1(LOC105377352):​n.1742A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 152,296 control chromosomes in the GnomAD database, including 86 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 0.029 (86 hom., cov: 32)
• Consequence: LOC105377352 NR_188418.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 9 publications found

Genes affected

LOC105377352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.029 (4421/152296) while in subpopulation NFE AF = 0.0393 (2669/67984). AF 95% confidence interval is 0.038. There are 86 homozygotes in GnomAd4. There are 2103 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 86 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188418.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377352	NR_188418.1		n.1742A>G		non_coding_transcript_exon	Exon 5 of 5
	LOC105377352	NR_188421.1		n.1596A>G		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 4419 AN: 152178 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00748

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0393

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0290 AC: 4421 AN: 152296 Hom.: 86 Cov.: 32 AF XY: 0.0282 AC XY: 2103 AN XY: 74472

African (AFR) AF: 0.00748 AC: 311 AN: 41592

American (AMR) AF: 0.0332 AC: 508 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0157 AC: 76 AN: 4830

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0393 AC: 2669 AN: 67984

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0378 Hom.: 384

Bravo AF: 0.0280

Asia WGS AF: 0.00751 AC: 27 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7669317; hg19: chr4-106457330;