4-102778621-T-C

Variant names:

• chr4-102778621-T-C
• rs223469
• XR_007058208.1:n.1936A>G

Variant summary

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

The XR_007058208.1(LOC124900743):​n.1936A>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 0.987 in 152,322 control chromosomes in the GnomAD database, including 74,131 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 0.99 (74131 hom., cov: 31)
• Consequence: LOC124900743 XR_007058208.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 6 publications found

Genes affected

LOC124900743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900743	XR_007058208.1	n.1936A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC102723704	NR_125932.1	n.713-187T>C		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.986 AC: 150149 AN: 152204 Hom.: 74071 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.985

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

GnomAD4 genome AF: 0.987 AC: 150268 AN: 152322 Hom.: 74131 Cov.: 31 AF XY: 0.988 AC XY: 73582 AN XY: 74490

African (AFR) AF: 0.996 AC: 41387 AN: 41568

American (AMR) AF: 0.991 AC: 15155 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3259 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.982 AC: 4742 AN: 4830

European-Finnish (FIN) AF: 0.998 AC: 10595 AN: 10620

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66730 AN: 68038

Other (OTH) AF: 0.985 AC: 2082 AN: 2114

Alfa AF: 0.984 Hom.: 10714

Bravo AF: 0.987

Asia WGS AF: 0.987 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs223469; hg19: chr4-103699778;