NM_198941.3:c.*39-133T>C

Variant names:

• chr20-44496488-A-G
• rs7270791
• NM_198941.3:c.*39-133T>C

Variant summary

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

The NM_198941.3(SERINC3):​c.*39-133T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,118 control chromosomes in the GnomAD database, including 2,831 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 0.17 (2831 hom., cov: 32)
  • Exomes 𝑓: 0.15 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: SERINC3 NM_198941.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 8 publications found

Genes affected

SERINC3 (HGNC:11699): (serine incorporator 3) Predicted to enable L-serine transmembrane transporter activity. Involved in defense response to virus; detection of virus; and innate immune response. Predicted to be located in Golgi apparatus. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERINC3	NM_198941.3	c.*39-133T>C		intron_variant	Intron 10 of 10		NP_945179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERINC3	ENST00000255175.5	c.*39-133T>C		intron_variant	Intron 10 of 10	5		ENSP00000255175.1
SERINC3	ENST00000411544.5	c.*39-133T>C		intron_variant	Intron 4 of 4	3		ENSP00000414197.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25868 AN: 152000 Hom.: 2813 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.163

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.148 AC: 18 AN: 122 Hom.: 1 AF XY: 0.139 AC XY: 10 AN XY: 72

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.143 AC: 14 AN: 98

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.182 AC: 4 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.170 AC: 25926 AN: 152118 Hom.: 2831 Cov.: 32 AF XY: 0.170 AC XY: 12609 AN XY: 74384

African (AFR) AF: 0.314 AC: 13030 AN: 41464

American (AMR) AF: 0.145 AC: 2213 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3468

East Asian (EAS) AF: 0.113 AC: 587 AN: 5184

South Asian (SAS) AF: 0.182 AC: 876 AN: 4820

European-Finnish (FIN) AF: 0.0906 AC: 960 AN: 10592

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7408 AN: 67990

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.136 Hom.: 910

Bravo AF: 0.179

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7270791; hg19: chr20-43125129;